Mammalian hibernation proceeds alongside a wide range of complex brain adaptive changes that appear to protect the brain from extreme hypoxia and hypothermia. Using immunofluorescence, confocal microscopy, quantitative analysis methods and intracellular injections, we have characterized microglia morphological changes that occur in the neocortex and hippocampus of the Syrian hamster during hibernation. In euthermic hamsters, microglial cells showed the typical ramified/resting morphology with multiple long, thin and highly-branched processes homogeneously immunostained for Iba-1. However, during torpor, microglial cell process numbers increase significantly accompanied by a shortening of the Iba-1 immunoreactive processes, which show a fragmented appearance. Adaptative changes of microglial cells during torpor coursed with no expression of microglial cell activation markers. We discuss the possibility that these morphological changes may contribute to neuronal damage prevention during hibernation.